Helicobacter pylori chronically infect the human stomach of 50% of the population worldwide. Ten to 30% of those infected will present with severe disease including peptic ulcers and gastric cancers15. H. pylori associated diseases cannot be attributed solely to expression of particular bacterial toxins. Instead, our overall working hypothesis is that H. pylori disease is a by-product of the interaction between bacterial factors necessary for establishing and maintaining infection and the resultant host defenses. This interaction is dynamic with both the bacteria and host changing over decades of infection. To study this complex process, we utilize a mouse model of infection and study genetic variation among isolates from human clinical populations. Our in vivo screen for H. pylori colonization genes in the previous funding period showed 29% of genes tested had a colonization defect and 60% of our colonization genes showed strain specific phenotypes16. This analysis, of over half of the genome, confirmed pathways previously implicated, but also identified unexpected and less well studied classes of genes, including genes involved in DNA uptake and modification plus a large number of hypothetical proteins (81). In our renewal we focus on completing our global analysis of genes contributing to stomach colonization and explore the mechanisms by which genes involved in natural competence for DNA transformation and recombination-based DNA repair promote infection. H. pylori's natural competence allows recombination between super-infecting strains to generate new genotypes during infection and spread of new alleles generated within a strain population. We will explore the roles DNA exchange and recombination-based repair may play during infection of a single strain including 1.) repair of DNA damage encountered during infection 2.) generation of adaptive genetic variation and 3). catalysis of genetic switching events affecting the expression of genes promoting (or limiting) colonization. Our efforts to fully map the genes contributing to virulence will identify the mediators of persistent infection and studies of genetic variation in the clinical population will show how these mediators adapt during chronic inflammation that is associated with infection and leads to severe disease (ulcer, cancer). Our study of the mechanisms by which H. pylori promotes genetic exchange and diversification should also increase understanding of the spread of antimicrobial resistance, an increasing clinical problem in the treatment of H. pylori. This fits the mission of NIAID to understand and treat infectious diseases.